One of the notions implicit in most evolutionary models is that the tree of life has a common root. In other words all individuals of all species represent end points of lineages which ultimately coalesce back to the the original common ancestor. The first Earthling, so to speak. I say implicit because common ancestry isn’t necessary for evolution to be valid; after all, we presumably accept that evolutionary process is operative in an exobiological context, if such a context exists. Therefore it is possible that modern extant lineages are derived from separate independent antecedents. A “multiple garden” model. This has seemed less and less plausible as the molecular basis of biology has been elucidated; it looks like the basic toolkit is found all across the tree of life. But with a new found awareness of the power of processes such as horizontal gene transfer the open & shut case is faced with a new element of ambiguity. Or perhaps not?

Here’s a post from Wired, Life on Earth Arose Just Once:

The idea that life forms share a common ancestor is “a central pillar of evolutionary theory,” says Douglas Theobald, a biochemist at Brandeis University in Waltham, Massachusetts. “But recently there has been some mumbling, especially from microbiologists, that it may not be so cut-and-dried.”

Because microorganisms of different species often swap genes, some scientists have proposed that multiple primordial life forms could have tossed their genetic material into life’s mix, creating a web, rather than a tree of life.

To determine which hypothesis is more likely correct, Theobald put various evolutionary ancestry models through rigorous statistical tests. The results, published in the May 13 Nature, come down overwhelmingly on the side of a single ancestor.

A universal common ancestor is at least 10^2,860 times more probable than having multiple ancestors, Theobald calculates.

The paper is now on the Nature website, A formal test of the theory of universal common ancestry. They looked specifically at 23 very conserved proteins across 12 taxa from the three domains of life (those being eukaryotes, prokaryotes, and the archaea). Here’s where the author explains the philosophy behind the statistical technique: Read More

Ancient DNA set to rewrite human history. Good overview by Rex Dalton at Nature. I assume he knows more than he’s letting on, so a bit of Kremlinology: “In March, the group reported the mitochondrial DNA sequence from this individual, an unknown hominin that, so far, does not genetically match either Neanderthals or H. sapiens and may represent a new species. The team dated the bone to about 40,000 years ago, but others say that the sediments around the bone may be as old as 100,000 years. There is speculation that the bone could be the remains of an older species of Homo, perhaps even of a remnant population of Homo heidelbergensis, known in Europe from 300,000 to 500,000 years ago, or of Homo erectus, found as early as 1.8 million years ago from Africa to Indonesia. A full sequence may help to resolve this.” I think we’ll know a lot more about X-woman and how she relates to us in the near future.

State IQ estimates (2009). Again, proximity to the Canadian border is a boon.

Neanderthals’r’us? A paleoanthropologist’s view. He claims that the genetics is finally aligning with the fossils.

The Neandertal fraction. John Hawks explains what it means to say that 1-4% of non-African ancestry is Neandertal when we always talk about how we’re 98-99% identical to chimpanzees. This came up in the comments but I didn’t address it because a little thought makes this pretty obvious, but now you can read John Hawks’ explanation if you need a boost.

Below is a video of the assault on a Swedish artist who drew Muhammad as a dog. He was at a university event celebrating free speech. People are shouting“Allahu Akbar!” Charming.
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Mirrored from http://wiringthebrain.blogspot.com

Why are genetically identical monozygotic twins not phenotypically identical? They are obviously much more similar than people who do not share all their DNA, but even in outward physical appearance are not really identical. And when it comes to psychological traits or psychiatric disorders, they can be quite divergent (concordance between monozygotic twins for schizophrenia for example is only around 50%). What is the source of this phenotypic variance? Why are the effects of a mutation often variable, even across genetically identical organisms?

“Nurture” has been the answer proffered by many, but there is good evidence that environmental or experience-dependent effects can not explain all the extra phenotypic variance and in most cases contribute very little to it. (See post on “Nature, nurture and noise” on June 24th, 2009 for more on this: http://wiringthebrain.blogspot.com/2009/06/nature-nurture-and-noise.html).
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Carl Zimmer asks “Will Anyone In Alabama Speak For Evolution?” The story is that a Republican candidate for governor in Alabama is being accused of not being a Creationist, and he is asserting that he is a Creationist. Some people might be surprised by this, but this is Alabama. It is famously well known that the general public tends to split down the middle in regards to evolution, and that there is a class aspect to the division. But what’s the breakdown by region? The GSS can help.

Let’s look at two variables:

SCITEST4: In your opinion, how true is this? Human beings developed from earlier species of
animals

REGION, which you can see on the Census Division map below:
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Economists in the last few years have been shifting toward testing their theoretical models, whether through the experiments of behavioral economics, or, “natural experiments.” The reason economists have had issues with testing their models is that experimentation on humans has some natural constraints. Macroeconomists have an even greater problem, as experimentation on whole societies not only presents ethical conundrums, but there’s no way to fund or implement experiments on this scale. Macroeconomists turn out to be the paleontologists of economics.

Of course economists aren’t the only ones who’ve had this sort of problem with humans. The reason that geneticists focused on organisms such as flies, mice and fish is partly that these taxa breed fast and are easy to maintain in laboratories. But obviously there are things you can do, such as mutagenesis, with model organisms which you can not do with humans. Human genetics has traditionally relied on “natural experiments” of a sort, inbred lineages, recurrent recessive diseases, etc. Genetics has been a supplementary handmaid to medicine by and large. But sometimes history can load the die in genetics’ favor as well.

During the “Columbian Exchange” the New and Old World engaged in a massive transfer of ideas and individuals. The Old World received potatoes, maize, and tomatoes (to name a few). The New World…well, the New World received black people and white people. As documented in works such as 1491 the indigenous populations of the New World collapsed with the introduction of Old World diseases. Native peoples disappeared from the Caribbean, and were marginalized on the mainland excepting ecologically remote (e.g., the Guatemalan highlands) or forbidding (e.g., the Peruvian highlands) regions. But of course despite the obliteration of indigenous cultural self-consciousness and identity, the native populations did not totally disappear, they persisted genetically in the numerically dominant mestizo populations of much of Latin America. You don’t need genetics to understand what happened, books like Mestizaje in Ibero-America outline in detail using conventional historical archives how Spanish men arrived in New World and entered into relationships with indigenous women. Often several at a time, in contravention of the Catholic Church’s requirement of monogamy.

But in the post-genomic era we have more to go on than impressions, we can quantitize the extent and nature of the admixture, something of importance when considering medical research. A new paper in PNAS adds some more to the growing body of results on Latin American genomics by including populations which have traditionally been overlooked, and also putting a spotlight on the long term impact of sex-biased admixture. Genome-wide patterns of population structure and admixture among Hispanic/Latino populations:
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Templeton disproves gene analysis that appeared to support out-of-Africa replacement model. This is from a Washington U. press release, but the title is still obnoxious. The term “prove” and “disprove” should be used sparingly in science (though perhaps there are others out there who disagree, I’d like some reasons laid out for why they shouldn’t be used only in exceptional circumstances). Remember that I pointed to a controversy between Alan Templeton and computational biologists who used a Bayesian phylogenetic framework a few weeks ago. Templeton is claiming that the Neandertal admixture findings vindicate him. Certainly one does need to revisit models which assume that admixture may have occurred, but only below a threshold of 1%, when the current research indicates 1% to be the low bound. But I don’t think we need to fall into the trap of separating the world into the light and the dark; people may be right for the wrong reasons, and methods may be wrong because of faulty axioms. And who knows, Paabo & company may be in error. It happens.

Koch Industries distances itself from tea parties. I wonder if the renewed focus on immigration is prompting this (the Koch’s are conventional libertarians on the issue, most Tea Party activists are not).

Obesity Linked to Lowest Earnings.

Animals Talk, Sing and Act Like Humans? Young Children’s Reasoning About Biological World Is Influenced by Cultural Beliefs. Psychologists get criticized for characterizing the minds of Western university students as universal, but in this case, they over-extrapolated from urban children.

The Psychological Diversity of Mankind. Like the rational actor model of economics there is some utility in focusing on the interindividual invariant aspects of cognition. But at some point you’ve squeezed all the juice out, and need to move on. Those of us who tend toward the neuroatypical side have intuitively understood that humans exhibit psychological diversity, because we’ve been looking in from outside the circus tent, whether we know it or not.

With the detection of Neanderthal admixture in Eurasians (Green et al), evidence for two admixture events in an upcoming paper from Jeffrey Long’s group (probably Neanderthals and erectus), and analysis from Jeffrey Wall and Vincent Plagnol suggesting that some African populations (Pygmies and Bushmen) admixed with other archaic populations, it seems that we are on the verge of a new paradigm.* In the picture, anatomically modern humans arose in East Africa and then spread globally – but mixed (to a degree) with the archaic humans that already already occupied most of the Old World.
Of course this is the surprise-free prediction, much more plausible than total replacement, which would have required an unlikely biological incompatibility.

Admixture at the few-percent level would have given most favorable archaic alleles a good chance of reaching high frequency in modern human populations, and some must have done so – alleles that conferred regional adaptations, and perhaps some that had general advantages. Svante Paabo thinks, or any rate says, that this Neanderthal admixture probably didn’t have any biological significance, but he’s almost certainly wrong.
This pattern has been seen in some other invasive species: the cosmopolitan species assimilates favorable alleles from local sister species. Resistance is futile.

There may be more in the pipeline: The Max Planck people have that strange finger bone from the Altai, and if it’s a good-enough sample, they could run the same general analysis and check for admixture from that archaic population, whoever they were. And there’s a possibly-significant line in their Science paper, concerning Wall and Plagnol’s high estimate (14%) of archaic admixture in Europeans:
“almost an order of magnitude greater than our estimates, suggesting that their observations may
not be entirely explained by gene flow from Neandertals. ” Maybe from somebody else?

*Mike Hammer and others have also been saying this.

There’s a very long review out which presents a theory for how sauropod dinosaurs could scale up to such enormous sizes, Biology of the sauropod dinosaurs: the evolution of gigantism. ScienceDaily is promoting the likelihood that sauropods did not chew, and so could make do with very small heads which could be supported by long necks, as the big factor. But this is a model with many moving parts. Here’s the verbal list from the conclusion:

(1) Sauropod dinosaurs as the largest terrestrial animals ever represent a challenge to evolutionary biologists trying to understand body size evolution.

(2) The study of the upper limit of body size must address extrinsic as well as intrinsic factors, and it must be determined whether this limit is set by the bauplan of the organisms or by physical and ecological constraints imposed by the environment. Among several possible approaches, we chose the resource perspective because it has been shown that resource availability and maximal body size correlate closely (Burness et al., 2001).

(3) In the interplay of the biology of sauropod dinosaurs with their environment, a unique combination of plesiomorphic features (i.e., inherited from their ancestors) and evolutionary novelties emerge as the key for a more efficient use of resources by sauropods than by other terrestrial herbivore lineages. Plesiomorphic features of sauropods were many small offspring, the lack of mastication and the lack of a gastric mill. The evolutionary innovations were an avian-style respiratory system and a high basal metabolic rate.

(4) We posit that the long neck of sauropods was central to the energy-efficient food uptake of sauropods because it permitted food uptake over a large volume with a stationary body.

(5) In the Late Triassic and Early Jurassic (210–175 million years ago), the combination of biological properties listed above led to an evolutionary cascade in the sauropodomorph lineage characterized by selection for ever larger body size, mainly driven by predation pressure from theropod dinosaurs.

(6)From the Middle Jurassic onward, sauropod dinosaurs dominated global terrestrial ecosystems only to succumb to the catastrophic environmental change at the end of the Cretaceous 65 million years ago.

And here’s a schematic illustrating the interplay of evolutionary forces & constraints:
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One of the most successful achievements of the “post-genomic era” has been the elucidation of the genetic architecture which undergird the variation in human pigmentation. I like to point out that in 2005 the geneticist Armand Leroi observed in his book Mutants that we didn’t know the genetics of normal variation in relation to the trait of skin color. In 2010 one couldn’t plausibly write that. We know the genes which control the vast majority of the interpopulational variation in human complexion. This is not due to human ingenuity, but the fortuitous hand that nature dealt us. Pigmentation is a very salient phenotype, evident by the classification of genetically very distinct populations in Africa, India and Oceania as “black.” But in terms of a genetic research project it has long been one of the ways to explore patterns of inheritance in model organisms such as mice, in particular in relation to coat patterns and pigment. And luckily for us, many of the genes which are implicated in pigment variation produce similar changes across diverse taxa. Additionally, the genetic architecture of human pigmentation variation is such that most of the variance is concentrated among a few loci of large effect. Concretely, it seems that well over 50% of the African-European difference in skin color as measured by reflectance of visible light is attributable to two genes, SLC24A5 and KITLG. In Europeans around 75% of the dichotomous variation between those with blue and non-blue eyes may be due to changes in the genomic region across HERC2 and OCA2 (these two genes are very near each other). These are the veritable low hanging fruit, amenable to studies with even small sample sizes and modest statistical power, so strong are the effects of the genetic variables.

And why is pigment important? Obviously there are social ramifications. But pigmentation is likely a major target of natural selection as well, as I suggested in relation to Neandertals. The results are sometimes confusing, but it does seem that pigmentation related loci are enriched in relation to those genomic regions which turn up as positive in tests of natural selection. Additionally, looking at variation around those genes which are correlated with lighter skin across Eurasia it also seems that it may be that our own lineage has become somewhat paler within the last 20,000 years, perhaps even more recently. And the same may have been true for our possible Neander-kin.

At the current rate in regards to pigmentation the age of revolutionary science may soon be over. Extraction of ancient DNA will probably resolve the rate and nature of evolutionary change, while further typing of current populations will flesh out our understanding of the variants responsible for normal human variation. To do that requires more than simply larger sample sizes or improved genomic techniques, it also requires better measurement. The utilization of reflectance indices in studies of study skin color are a step in the right direction, but a new paper in PLoS Genetics points the way toward the same in the study of eye color, Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci:
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If you haven’t checked out the “How It Should Have Ended” website, I really recommend it. I’m not a big consumer of web video excepting South Park and The Onion, but this is really good stuff. In particular this alternative ending of the original Iron Man is pretty amusing.